rs9442235

chr1-16066862-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_182623.3(FAM131C):c.23-3226A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 152,086 control chromosomes in the GnomAD database, including 19,041 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.49 (19041 hom., cov: 33)
• Consequence: FAM131C NM_182623.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

FAM131C (HGNC:26717): (family with sequence similarity 131 member C)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM131C	NM_182623.3	c.23-3226A>C		intron_variant		ENST00000375662.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM131C	ENST00000375662.5	c.23-3226A>C		intron_variant		1	NM_182623.3	P1
FAM131C	ENST00000494078.1	n.213-4328A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74363 AN: 151968 Hom.: 19013 Cov.: 33

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.0125

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.475

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.489 AC: 74426 AN: 152086 Hom.: 19041 Cov.: 33 AF XY: 0.482 AC XY: 35847 AN XY: 74342

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.0127

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.475

Alfa AF: 0.490 Hom.: 39999

Bravo AF: 0.500

Asia WGS AF: 0.260 AC: 906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.4
Dann	Benign	0.51

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9442235; hg19: chr1-16393357;